Vortex in this case is just another program running in the background, eating up system resources, that might be needed for Skyrim... Set up your mods in Vortex, then close it and start the game with "SKSE64_loader.exe". BTW
Tannin discontinued the project when he was hired by the Nexus team to develop their new Vortex mod manager. MO2 was not completed and was left with many issues. LePresidente managed to fix it to a usable state by himself after SkyrimSE came out, adding support for it, and releasing v...